R: Order Link Communities According to the Dendrogram

orderCommunities {linkcomm} | R Documentation

## Order Link Communities According to the Dendrogram

### Description

This function returns link communities in the same order as in the hierarchical clustering dendrogram.

### Usage

    orderCommunities(x, clusterids = 1:x$numbers[3], verbose = TRUE)

### Arguments

`x` | An object of class `linkcomm`.
`clusterids` | An integer vector of community IDs. Defaults to all communities.
`verbose` | Logical, whether to print progress of the calculation to the screen. Defaults to TRUE.

### Details

Ordering link communities according to the dendrogram can aid in visualization when plotting them as a Spencer circle because it minimses crossing over between links.

### Value

A list with the following components:

`ordered` | A list of integer vectors. These are the ordered communities of links.
`clusids` | An integer vector of community IDs in their new order.

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

### See Also

`plot.linkcomm`, `plotLinkCommGraph`

### Examples

    ## Generate graph and extract link communities.
    g <- swiss[,3:4]
    lc <- getLinkCommunities(g)

    ## Order communities according to the dendrogram.
    orderCommunities(lc)

[Package linkcomm version 1.0-14 Index]